PhD Scholarship: Discovering the Chemical Signals that Activate Hidden Phages

Description

A PhD scholarship is available within Professor Robert Edwards’ ARC Laureate Fellowship program, “New Horizons for Synthetic Phages”, at Flinders University.

Many bacteria contain dormant phages, known as prophages, hidden within their genomes. These phages can respond to environmental signals and switch from a dormant state to active replication, killing their bacterial hosts. However, we know very little about the signals that most phages detect, the proteins that sense those signals, or how these regulatory systems could be used to control synthetic phages.

This PhD project will investigate how microbial communities and bacterial isolates respond to chemical signals that induce phage activation. The candidate will use high-throughput assays, flow cytometry, anaerobic culturing, phage induction experiments, DNA sequencing, and metagenomics to identify compounds that activate prophages. Candidate signals may include antibiotics, microbial metabolites, oxidative stress compounds, short-chain fatty acids, polyphenols, and drug-like chemical scaffolds.

The project will also link experimental phage-induction data with genomic and metagenomic analyses to identify which phages respond to specific compounds and which phage-encoded proteins may detect those signals. These discoveries will help establish new ways to control phage behaviour, including the future design of synthetic phages that respond to defined environmental cues.

Benefits

The scholarship includes:

• A stipend at the University’s standard rate (currently $36,061 per year), indexed annually, for 3.5 years.
• Tuition fee offset or waiver, subject to eligibility and scholarship conditions.
• Support for project expenses, computing, data analysis, software development, and research training.
• Training in in microbiology, phage biology, molecular biology, DNA sequencing, and bioinformatics.
• Access to advanced laboratory infrastructure, including microbial culturing, sequencing, and cytometry platforms.
• Opportunities to work in a highly interdisciplinary team spanning microbiology, bioinformatics, synthetic biology, and computational biology.
• Opportunities to present research at national and international conferences.
• Networking and training through the Laureate Fellowship, Flinders microbiome research community, and international phage research networks.

Eligibility

To be eligible, applicants must:

• Meet Flinders University PhD admission requirements, normally through Honours I/IIA, a Master’s degree, or equivalent research experience.
• Be eligible to enrol as a full-time PhD candidate at Flinders University.
• Be able to take up the scholarship within 3 months of the offer, unless an extension is approved.
• Be physically based at Flinders University for the duration of the candidature. 
• Meet any relevant institutional, biosafety, ethics, or background-check requirements associated with laboratory-based microbiology and molecular biology research.

All PhD projects are full-time. No positions are remote-only. Candidates must be physically based at Flinders University to ensure a strong, collaborative cohort is developed across the Laureate Fellowship program. Candidates will be expected to participate actively in laboratory meetings, cohort activities, research training, workshops, and relevant national or international conferences.